Publications by authors named "Sofia Robb"

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The Unified Phenotype Ontology : a framework for cross-species integrative phenomics.
Nicolas Matentzoglu, Susan M Bello, Ray Stefancsik, Sarah M Alghamdi, Anna V Anagnostopoulos, Sofia M C Robb

Genetics· March 2025

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Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI).
Sabrina Toro, Anna V Anagnostopoulos, Susan M Bello, Kai Blumberg, Rhiannon Cameron, Sofia Mc Robb

J Biomed Semantics· October 2024

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Sugar assimilation underlying dietary evolution of Neotropical bats.
Jasmin Camacho, Andrea Bernal-Rivera, Valentina Peña, Pedro Morales-Sosa, Sofia M C Robb

Nat Ecol Evol· September 2024

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(veiled chameleon) chromosome-scale genome assembly and annotation provides insights into the evolution of reptiles and developmental mechanisms.
Natalia A Shylo, Andrew J Price, Sofia Robb, Richard Kupronis, Irán Andira Guzmán Méndez

bioRxiv· September 2024

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The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics.
Nicolas Matentzoglu, Susan M Bello, Ray Stefancsik, Sarah M Alghamdi, Anna V Anagnostopoulos, Sofia Mc Robb

bioRxiv· September 2024

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Topological structures and syntenic conservation in sea anemone genomes.
Bob Zimmermann, Juan D Montenegro, Sofia M C Robb, Whitney J Fropf, Lukas Weilguny

Nat Commun· December 2023

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An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes.
Nataliya Timoshevskaya, Kaan I Eşkut, Vladimir A Timoshevskiy, Sofia M C Robb, Carson Holt, Robb Krumlauf

Cell Rep· March 2023

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Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies.
Nicolas Matentzoglu, Damien Goutte-Gattat, Shawn Zheng Kai Tan, James P Balhoff, Seth Carbon, Sofia Mc Robb

Database (Oxford)· October 2022

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Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms.
Stephanie H Nowotarski, Erin L Davies, Sofia M C Robb, Eric J Ross, Nicolas Matentzoglu

Development· August 2021

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Genomic diversity generated by a transposable element burst in a rice recombinant inbred population.
Jinfeng Chen, Lu Lu, Sofia M C Robb, Matthew Collin, Yutaka Okumoto

Proc Natl Acad Sci U S A· October 2020

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Changes in regeneration-responsive enhancers shape regenerative capacities in vertebrates.
Wei Wang, Chi-Kuo Hu, An Zeng, Dana Alegre, Deqing Hu, Sofia Robb

Science· September 2020

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The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.
Kent A Shefchek, Nomi L Harris, Michael Gargano, Nicolas Matentzoglu, Deepak Unni, Sofia Robb

Nucleic Acids Res· January 2020

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Publisher Correction: The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution.
Jeramiah J Smith, Nataliya Timoshevskaya, Chengxi Ye, Carson Holt, Melissa C Keinath, Sofia M C Robb, Robb Krumlauf

Nat Genet· November 2018

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Phylogenetic and Phylogenomic Definition of Species.
Andrii P Gryganskyi, Jacob Golan, Somayeh Dolatabadi, Stephen Mondo, Sofia Robb

G3 (Bethesda)· May 2018

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Publisher Correction: The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution.
Jeramiah J Smith, Nataliya Timoshevskaya, Chengxi Ye, Carson Holt, Melissa C Keinath, Sofia M C Robb, Robb Krumlauf

Nat Genet· May 2018

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The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution.
Jeramiah J Smith, Nataliya Timoshevskaya, Chengxi Ye, Carson Holt, Melissa C Keinath, Sofia M C Robb, Robb Krumlauf

Nat Genet· February 2018

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Cellular, ultrastructural and molecular analyses of epidermal cell development in the planarian Schmidtea mediterranea.
Li-Chun Cheng, Kimberly C Tu, Chris W Seidel, Sofia M C Robb, Fengli Guo

Dev Biol· January 2018

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Tracking the genome-wide outcomes of a transposable element burst over decades of amplification.
Lu Lu, Jinfeng Chen, Sofia M C Robb, Yutaka Okumoto, Jason E Stajich

Proc Natl Acad Sci U S A· December 2017

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SmedGD 2.0: The Schmidtea mediterranea genome database.
Sofia M C Robb, Kirsten Gotting, Eric Ross, Alejandro Sánchez Alvarado

Genesis· August 2015

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Histone modifications and regeneration in the planarian Schmidtea mediterranea.
Sofia M C Robb, Alejandro Sánchez Alvarado

Curr Top Dev Biol· October 2014

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The use of RelocaTE and unassembled short reads to produce high-resolution snapshots of transposable element generated diversity in rice.
Sofia M C Robb, Lu Lu, Elizabeth Valencia, James M Burnette, Yutaka Okumoto

G3 (Bethesda)· June 2013

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SmedGD: the Schmidtea mediterranea genome database.
Sofia M C Robb, Eric Ross, Alejandro Sánchez Alvarado

Nucleic Acids Res· January 2008

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MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes.
Brandi L Cantarel, Ian Korf, Sofia M C Robb, Genis Parra, Eric Ross

Genome Res· January 2008

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The Schmidtea mediterranea database as a molecular resource for studying platyhelminthes, stem cells and regeneration.
Alejandro Sánchez Alvarado, Phillip A Newmark, Sofia M Robb, Réjeanne Juste

Development· December 2002

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